Extract AVGX_V2
patch03 folder goes into GxpPacker
moacode folders into MwbExtractor
The only things you should note is you need to duplicate the moacode.mwb from the patch03 and place in MwbExtractor.
After that after editing the translation files in the moacode folder you just drag that folder to MwbExtractor.exe(needs moacode.mwb to be present otherwise you get error) and it will update it.
After that you replace moacode.mwb in the patch03 and do the same with GxpPacker.exe, it already has the right structure.
What you should note is you can get bugs if you exceed the line numbers of the original in "some" scripts.
But you shouldn't worry too much as if it was the case for every script the game would have been completely fucked.
At the ending there is probably more script triggers around.
I am not sure about the heroine capture, it could just be you need to be further into the story to properly capture. I haven't managed to get the mage to join after I let go once, do you know how that plays out? since I am wondering if my tinkering caused another bug.
Usually scripts start just fine, it's when they end bugs appear, and scripts that are chained with previous script. Can you give a previous save where a previous story scene played? I could look into that.
Edit: Updated the MTL for now.